\hypertarget{classbuild__string}{
\section{build\_\-string Class Reference}
\label{classbuild__string}\index{build\_\-string@{build\_\-string}}
}


Produces a row of chars for the protein given.  




{\ttfamily \#include $<$build\_\-string.h$>$}

\subsection*{Public Member Functions}
\begin{DoxyCompactItemize}
\item 
\hypertarget{classbuild__string_a19419eab161e1efd271b10b261f70c4f}{
void \hyperlink{classbuild__string_a19419eab161e1efd271b10b261f70c4f}{write\_\-data\_\-to\_\-file} (FILE $\ast$out\_\-file, const bool PIPE)}
\label{classbuild__string_a19419eab161e1efd271b10b261f70c4f}

\begin{DoxyCompactList}\small\item\em Writes the string to the file, and clears the memory. \end{DoxyCompactList}\item 
\hypertarget{classbuild__string_a50d30ff1b5907505f1bb6c0dcfb2bdf1}{
void \hyperlink{classbuild__string_a50d30ff1b5907505f1bb6c0dcfb2bdf1}{setHeader} (uint world\_\-index\_\-in)}
\label{classbuild__string_a50d30ff1b5907505f1bb6c0dcfb2bdf1}

\begin{DoxyCompactList}\small\item\em Sets the header for the string to be written to the output file. \end{DoxyCompactList}\item 
\hypertarget{classbuild__string_aede88335fe17c08e79037062a643ebe3}{
void \hyperlink{classbuild__string_aede88335fe17c08e79037062a643ebe3}{avoidPrinting} ()}
\label{classbuild__string_aede88335fe17c08e79037062a643ebe3}

\begin{DoxyCompactList}\small\item\em Called when no data shall be printed to the stream. \end{DoxyCompactList}\item 
\hypertarget{classbuild__string_a98333ab6b8a689c1193484968034e4a2}{
void \hyperlink{classbuild__string_a98333ab6b8a689c1193484968034e4a2}{writeRow} (bool \_\-has\_\-data)}
\label{classbuild__string_a98333ab6b8a689c1193484968034e4a2}

\begin{DoxyCompactList}\small\item\em If set to true, the data in the poiners are written to a file. \end{DoxyCompactList}\item 
bool \hyperlink{classbuild__string_a52cafc5f26245fa4741566aabd6ddda0}{hasData} ()
\item 
char $\ast$ \hyperlink{classbuild__string_a37a1e89bb91897138559428e01fb35ac}{begin} ()
\item 
\hypertarget{classbuild__string_a17cb4ac597e6c69501066395dd91f75e}{
void \hyperlink{classbuild__string_a17cb4ac597e6c69501066395dd91f75e}{append} (char $\ast$first, char $\ast$last)}
\label{classbuild__string_a17cb4ac597e6c69501066395dd91f75e}

\begin{DoxyCompactList}\small\item\em Appends the chars to the buffer. \end{DoxyCompactList}\item 
void \hyperlink{classbuild__string_a34d1d576c008bf55a16f2d302f516f22}{copy} (char $\ast$start, char $\ast$end)
\begin{DoxyCompactList}\small\item\em adds the content of the input to the string located in this object. \end{DoxyCompactList}\item 
\hypertarget{classbuild__string_a6d482526f8327e8595137f0e9e7d687e}{
void \hyperlink{classbuild__string_a6d482526f8327e8595137f0e9e7d687e}{copy\_\-struct} (\hyperlink{classbuild__string}{build\_\-string} row)}
\label{classbuild__string_a6d482526f8327e8595137f0e9e7d687e}

\begin{DoxyCompactList}\small\item\em adds the content of the input to the string located in this object. \end{DoxyCompactList}\item 
\hypertarget{classbuild__string_a81409b0878da21f1086502e05a6ea05d}{
void \hyperlink{classbuild__string_a81409b0878da21f1086502e05a6ea05d}{end\_\-blast\_\-line} ()}
\label{classbuild__string_a81409b0878da21f1086502e05a6ea05d}

\begin{DoxyCompactList}\small\item\em Appends the line-\/end characters specified for the 'blast' file format. \end{DoxyCompactList}\item 
\hypertarget{classbuild__string_a992d7b129b663a9119e98b29ea4c8ad2}{
long int \hyperlink{classbuild__string_a992d7b129b663a9119e98b29ea4c8ad2}{getIndex} ()}
\label{classbuild__string_a992d7b129b663a9119e98b29ea4c8ad2}

\begin{DoxyCompactList}\small\item\em Returns the size of the index. \end{DoxyCompactList}\item 
\hypertarget{classbuild__string_a9e12cd7000135806bd6073e5aa867dbd}{
void \hyperlink{classbuild__string_a9e12cd7000135806bd6073e5aa867dbd}{finalize} ()}
\label{classbuild__string_a9e12cd7000135806bd6073e5aa867dbd}

\begin{DoxyCompactList}\small\item\em Appends the line end ('$\backslash$0' character) \end{DoxyCompactList}\item 
\hypertarget{classbuild__string_a2f3695b7e6a0075abe4417f193b3eaf2}{
uint \hyperlink{classbuild__string_a2f3695b7e6a0075abe4417f193b3eaf2}{size} ()}
\label{classbuild__string_a2f3695b7e6a0075abe4417f193b3eaf2}

\begin{DoxyCompactList}\small\item\em Length of sequence. \end{DoxyCompactList}\item 
mem\_\-loc \hyperlink{classbuild__string_abf31cdd8cf4dc39a75f22362f66ca139}{resize\_\-if\_\-to\_\-large} (mem\_\-loc length\_\-argument)
\begin{DoxyCompactList}\small\item\em Increases the size of the buffer if it does not fit. \end{DoxyCompactList}\item 
\hypertarget{classbuild__string_a13a4d89be52ace631744c302e2730a0f}{
void \hyperlink{classbuild__string_a13a4d89be52ace631744c302e2730a0f}{free\_\-mem} ()}
\label{classbuild__string_a13a4d89be52ace631744c302e2730a0f}

\begin{DoxyCompactList}\small\item\em Frees the memory allocated for this object. \end{DoxyCompactList}\item 
\hypertarget{classbuild__string_a052f287f040fd2869e979fa362018d18}{
\hyperlink{classbuild__string_a052f287f040fd2869e979fa362018d18}{build\_\-string} (uint \_\-size\_\-blast\_\-all)}
\label{classbuild__string_a052f287f040fd2869e979fa362018d18}

\begin{DoxyCompactList}\small\item\em The constructor. \end{DoxyCompactList}\end{DoxyCompactItemize}
\subsection*{Static Public Member Functions}
\begin{DoxyCompactItemize}
\item 
\hypertarget{classbuild__string_a5f4c6566dd3c3e865d7241f879bcfe23}{
static \hyperlink{classbuild__string}{build\_\-string} $\ast$ \hyperlink{classbuild__string_a5f4c6566dd3c3e865d7241f879bcfe23}{allocate\_\-class} (uint size)}
\label{classbuild__string_a5f4c6566dd3c3e865d7241f879bcfe23}

\begin{DoxyCompactList}\small\item\em Allocates a list of 'this' class, but do not initialize it. \end{DoxyCompactList}\end{DoxyCompactItemize}


\subsection{Detailed Description}
Produces a row of chars for the protein given. 

\begin{DoxyAuthor}{Author}
Ole Kristian Ekseth (oekseth 
\end{DoxyAuthor}
\begin{DoxyDate}{Date}
21.12.2010 by oekseth (initial) 

16.09.2011 by oekseth (asserts) 

31.12.2011 by oekseth (cleanup) 
\end{DoxyDate}


\subsection{Member Function Documentation}
\hypertarget{classbuild__string_a37a1e89bb91897138559428e01fb35ac}{
\index{build\_\-string@{build\_\-string}!begin@{begin}}
\index{begin@{begin}!build_string@{build\_\-string}}
\subsubsection[{begin}]{\setlength{\rightskip}{0pt plus 5cm}char$\ast$ build\_\-string::begin (
\begin{DoxyParamCaption}
{}
\end{DoxyParamCaption}
)}}
\label{classbuild__string_a37a1e89bb91897138559428e01fb35ac}
\begin{DoxyReturn}{Returns}
pointer to beginning of the sequence the string represents. 
\end{DoxyReturn}
\hypertarget{classbuild__string_a34d1d576c008bf55a16f2d302f516f22}{
\index{build\_\-string@{build\_\-string}!copy@{copy}}
\index{copy@{copy}!build_string@{build\_\-string}}
\subsubsection[{copy}]{\setlength{\rightskip}{0pt plus 5cm}void build\_\-string::copy (
\begin{DoxyParamCaption}
\item[{char $\ast$}]{start, }
\item[{char $\ast$}]{end}
\end{DoxyParamCaption}
)}}
\label{classbuild__string_a34d1d576c008bf55a16f2d302f516f22}


adds the content of the input to the string located in this object. 


\begin{DoxyParams}{Parameters}
{\em $<$start$>$} & Pointer to the first char in the sequence of chars. \\
\hline
{\em $<$end$>$} & Pointer to the last char in the sequence of chars. \\
\hline
\end{DoxyParams}
\hypertarget{classbuild__string_a52cafc5f26245fa4741566aabd6ddda0}{
\index{build\_\-string@{build\_\-string}!hasData@{hasData}}
\index{hasData@{hasData}!build_string@{build\_\-string}}
\subsubsection[{hasData}]{\setlength{\rightskip}{0pt plus 5cm}bool build\_\-string::hasData (
\begin{DoxyParamCaption}
{}
\end{DoxyParamCaption}
)}}
\label{classbuild__string_a52cafc5f26245fa4741566aabd6ddda0}
\begin{DoxyReturn}{Returns}
true if data shall be printed 
\end{DoxyReturn}
\hypertarget{classbuild__string_abf31cdd8cf4dc39a75f22362f66ca139}{
\index{build\_\-string@{build\_\-string}!resize\_\-if\_\-to\_\-large@{resize\_\-if\_\-to\_\-large}}
\index{resize\_\-if\_\-to\_\-large@{resize\_\-if\_\-to\_\-large}!build_string@{build\_\-string}}
\subsubsection[{resize\_\-if\_\-to\_\-large}]{\setlength{\rightskip}{0pt plus 5cm}mem\_\-loc build\_\-string::resize\_\-if\_\-to\_\-large (
\begin{DoxyParamCaption}
\item[{mem\_\-loc}]{length\_\-argument}
\end{DoxyParamCaption}
)}}
\label{classbuild__string_abf31cdd8cf4dc39a75f22362f66ca139}


Increases the size of the buffer if it does not fit. 


\begin{DoxyParams}{Parameters}
{\em $<$length\_\-argument$>$} & the length of the input. \\
\hline
\end{DoxyParams}
\begin{DoxyReturn}{Returns}
the size of the argument to be copied. 
\end{DoxyReturn}
\begin{DoxyRemark}{Remarks}
To be used at insertion of a new part of the char array 
\end{DoxyRemark}


The documentation for this class was generated from the following file:\begin{DoxyCompactItemize}
\item 
\hyperlink{build__string_8h}{build\_\-string.h}\end{DoxyCompactItemize}
